A network-based approach to identify substrate classes of bacterial glycosyltransferases

Background

Bacterial interactions with the environment- and/or host largely depend on the bacterial glycome. The specificities of a bacterial glycome are largely determined by glycosyltransferases (GTs), the enzymes involved in transferring sugar moieties from an activated donor to a specific substrate. Of these GTs their coding regions, but mainly also their substrate specificity are still largely unannotated as most sequence-based annotation flows suffer from the lack of characterized sequence motifs that can aid in the prediction of the substrate specificity.

Results

In this work, we developed an analysis flow that uses sequence-based strategies to predict novel GTs, but also exploits a network-based approach to infer the putative substrate classes of these predicted GTs. Our analysis flow was benchmarked with the well-documented GT-repertoire of Campylobacter jejuni NCTC 11168 and applied to the probiotic model Lactobacillus rhamnosus GG to expand our insights in the glycosylation potential of this bacterium. In L. rhamnosus GG we could predict 48 GTs of which eight were not previously reported. For at least 20 of these GTs a substrate relation was inferred.

Conclusions

We confirmed through experimental validation our prediction of WelI acting upstream of WelE in the biosynthesis of exopolysaccharides. We further hypothesize to have identified in L. rhamnosus GG the yet undiscovered genes involved in the biosynthesis of glucose-rich glycans and novel GTs involved in the glycosylation of proteins. Interestingly, we also predict GTs with well-known functions in peptidoglycan synthesis to also play a role in protein glycosylation.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-349) contains supplementary material, which is available to authorized users.     

The isolation of monoclonal antibodies to Cryptococcus neoformans antigens

In this work conditions for the reproduction of hybridoma technology, specially adapted to C. neoformans, for obtaining monoclonal hybridomas (McAb) to diagnostically significant antigens of C. neoformans, the infective agent of cryptococcosis, are presented. The advantages of using the short-time cycle of stimulation of mouse B lymphocytes with low doses of C. neoformans capsular polysaccharide and the effectiveness of the hybridization of mouse spleen cells with myeloma cells, line Sp2/0, are shown. Four lines of stable hybridomas, producing McAb to different epitopes of C. neoformans surface antigens, have been obtained. The specific activity of McAb has been studied in the indirect immunofluorescence assay, the cytochemical and solid-phase enzyme immunoassays (EIA). McAb 3E2, Cr2 and 2G9 have been shown to be suitable for use in diagnostic EIA systems.     

BSA Adsorption on Porous Scaffolds Prepared from BioPEGylated Poly(3-Hydroxybutyrate)

Porous scaffolds for tissue engineering have been prepared from poly(3-hydroxybutyrate) (PHB) and a copolymer of poly(3-hydroxybutyrate) and polyethylene glycol (PHB-PEG) produced by bioPEGylation. The morphology of the scaffolds and their capacity for adsorption of the model protein bovine serum albumin (BSA) have been studied. Scaffolds produced from bioPEGylated PHB adsorbed more BSA, whereas the share of protein irreversibly adsorbed on these scaffolds was significantly lower (33%) than in the case of PHB homopolymer-based scaffolds (47%). The effect of protein adsorption on scaffold biocompatibility in vitro was tested in an experiment that involved the cultivation of fibroblasts (line COS-1) on the scaffolds. PHB-PEG scaffolds had a higher capacity for supporting cell growth than PHB-based scaffolds. Thus, the bioPEGylated PHB-based polymer scaffolds developed in the present study have considerable potential for use in soft tissue engineering.     

Mitochondrial haplotype diversity in the tortoise species <Emphasis Type="Italic">Testudo graeca</Emphasis> from North Africa and the Middle East

Background  

To help conservation programs of the endangered spur-thighed tortoise and to gain better insight into its systematics, genetic variation and evolution in the tortoise species Testudo graeca (Testudines: Testudinidae) was investigated by sequence analysis of a 394-nucleotide fragment of the mitochondrial 12S rRNA gene for 158 tortoise specimens belonging to the subspecies Testudo graeca graeca, Testudo graeca ibera, Testudo graeca terrestris, and a newly recognized subspecies Testudo graeca whitei. A 411-nucleotide fragment of the mitochondrial D-loop was additionally sequenced for a subset of 22 T. graeca, chosen because of their 12S gene haplotype and/or geographical origin.     

Molecular determinants of caste differentiation in the highly eusocial honeybee <Emphasis Type="Italic">Apis mellifera</Emphasis>

Background  

In honeybees, differential feeding of female larvae promotes the occurrence of two different phenotypes, a queen and a worker, from identical genotypes, through incremental alterations, which affect general growth, and character state alterations that result in the presence or absence of specific structures. Although previous studies revealed a link between incremental alterations and differential expression of physiometabolic genes, the molecular changes accompanying character state alterations remain unknown.     

Solid-phase immunoenzyme analysis of Coccidioides immitis antigens

A highly effective and specific solid-phase enzyme immunoassay system has been developed. The enzyme immunoassay is a highly sensitive technique for the detection and identification of C. immitis cellular and metabolic antigens. This technique is suitable for the study of strain differences in the antigenic composition of C. immitis, rendered harmless by different methods. The expediency of the preliminary sonification of cell suspensions of C. immitis, the causative agent of coccidioidomycosis, has been experimentally confirmed.